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- PDB-9jbd: Crystal Structure of the MoaE-like domain within Rv3323c from Myc... -

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Basic information

Entry
Database: PDB / ID: 9jbd
TitleCrystal Structure of the MoaE-like domain within Rv3323c from Mycobacterium tuberculosis
ComponentsProbable MoaD-MoaE fusion protein MoaX
KeywordsTRANSFERASE / molybdopterin synthase / MoaX
Function / homology
Function and homology information


molybdopterin synthase / Mo-molybdopterin cofactor biosynthetic process / cytosol
Similarity search - Function
Molybdopterin biosynthesis MoaE / Molybdopterin biosynthesis MoaE subunit superfamily / MoaE protein / Sulfur carrier ThiS/MoaD-like / ThiS family / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / Beta-grasp domain superfamily
Similarity search - Domain/homology
Molybdopterin synthase catalytic subunit 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCho, H.J. / Yang, S.H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2021RIS-001 Korea, Republic Of
National Research Foundation (NRF, Korea)2022R1F1A1074091 Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2025
Title: Structural comparison of three MoaE proteins in Mycobacterium tuberculosis: Insights into molybdopterin synthase assembly and specificity.
Authors: Cho, H.J. / Yang, S.H. / Lee, H.S. / Kang, B.S.
History
DepositionAug 26, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable MoaD-MoaE fusion protein MoaX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2834
Polymers15,9041
Non-polymers3793
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-0 kcal/mol
Surface area7640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.015, 98.015, 102.940
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Probable MoaD-MoaE fusion protein MoaX / molybdopterin synthase


Mass: 15903.997 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MoaE like domain in MoaX protein
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: moaX, Rv3323c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6MWY3
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.49 Å3/Da / Density % sol: 72.59 %
Crystal growTemperature: 291.5 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 18% PEG 400, 0.04M Li2SO4, 0.1M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jun 18, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 11920 / % possible obs: 99.9 % / Redundancy: 18.8 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.016 / Rrim(I) all: 0.071 / Χ2: 0.893 / Net I/σ(I): 8.7 / Num. measured all: 223537
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.4-2.4418.30.9435740.9650.9910.2240.970.469100
2.44-2.4918.10.7435740.9710.9930.1780.7640.4799.7
2.49-2.5318.40.6425850.9790.9950.1530.6610.47899.7
2.53-2.5919.80.5535790.9870.9970.1260.5670.48199.8
2.59-2.6420.20.5095750.9870.9970.1140.5220.48499.8
2.64-2.719.80.3725740.9950.9990.0850.3820.511100
2.7-2.7719.50.2885730.9960.9990.0670.2960.5499.8
2.77-2.85190.3015970.9940.9990.0710.3090.54899.8
2.85-2.9317.80.1945830.9980.9990.0480.20.61499.8
2.93-3.0219.20.1525890.99910.0350.1560.61799.8
3.02-3.1320.20.1365790.99810.0310.140.768100
3.13-3.2619.90.1096020.99910.0250.1110.713100
3.26-3.4119.90.0875930.99910.020.0890.807100
3.41-3.5819.50.0715840.99910.0160.0720.968100
3.58-3.81190.066130.99910.0140.0611.124100
3.81-4.118.50.0545970.99910.0130.0561.341100
4.1-4.52170.0496060.99910.0120.0511.534100
4.52-5.1718.30.0466200.99910.0110.0471.708100
5.17-6.51170.0466290.99910.0110.0471.74299.8
6.51-5016.40.0426940.99910.0110.0431.99399.3

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Processing

Software
NameVersionClassification
PHENIX(???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→35.49 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2648 1182 10.01 %
Rwork0.2175 --
obs0.2223 11807 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→35.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1071 0 24 28 1123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.952
X-RAY DIFFRACTIONf_dihedral_angle_d17.777419
X-RAY DIFFRACTIONf_chiral_restr0.052168
X-RAY DIFFRACTIONf_plane_restr0.01199
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.510.35361410.2961274X-RAY DIFFRACTION98
2.51-2.640.29321440.26131282X-RAY DIFFRACTION99
2.64-2.810.31311420.24881291X-RAY DIFFRACTION99
2.81-3.030.31481450.24331310X-RAY DIFFRACTION99
3.03-3.330.28321470.23811314X-RAY DIFFRACTION100
3.33-3.810.27541490.2211345X-RAY DIFFRACTION100
3.81-4.80.21581510.20021350X-RAY DIFFRACTION100
4.8-35.490.26621630.19971459X-RAY DIFFRACTION100

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